


Evolution

by TwinEnigma



Series: What Makes You [2]
Category: Naruto
Genre: Alternate Universe, Brainwashing, Canon-Typical Violence, Clones, Conspiracy, GFY, Human Experimentation, Identity Issues, Implied/Referenced Brainwashing, Memory Alteration, Multi, Unethical Experimentation, cloning, everything's better with clones
Language: English
Status: In-Progress
Published: 2010-12-21
Updated: 2015-12-01
Packaged: 2018-04-15 07:52:57
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 4
Words: 4,770
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/4598793
Author URL: https://archiveofourown.org/users/TwinEnigma/pseuds/TwinEnigma
Summary: <blockquote class="userstuff">
              <p>After the war, two members of a covert squad struggle to find their identities and free themselves. All they know is that they are all clones of two people - one of whom was Sasuke Uchiha.</p>
            </blockquote>





	1. Prologue

                Isoji paused, wiping the sweat from his face with a rag. It was a hot day for this early in the season, especially for Fire Country, and there wasn’t a cloud in the sky to shield him from the heat of the sun. Some of his dark hair had already come loose from the pony tail he’d tied it in. It stuck, limp and heavy, against his skin. He adjusted his hat, an old beat-up thing that was nearly as shabby as his coveralls, and looked out across the field, squinting from the harsh glare.

                His heart nearly skipped a beat.

                On the other side of his fence stood a figure in a black, hooded cloak, watching him from the dirt road with an eerie stillness.

                Despite the heat, Isoji felt the hair on the back of his neck prickle with a sudden chill.

                The small farm he and his wife, Juniko, called home was well off the beaten path, located on the hilly fringes of a sparsely populated farming town and accessible only by a small, rough dirt road that was notoriously easy to miss. It was tiny, tucked away from even their closest neighbors, with only a small single-level house and barn perched on the crest of a gently rolling hill that overlooked their fields, and surrounded by dense tree cover. They’d picked this place for its privacy and for nearly a decade and a half after the War, they’d had just that. Even the occasional shinobi passed this place by without so much as a second glance.

                And now, after all these years – Sage’s balls, Otoyoshi had _warned_ all of them this was a possibility, but he’d been sure and they’d gone so far off the grid…

                Isoji tightened his grip on the handle of his spade and raised his head, approaching the fence. Inwardly, he prayed that he was wrong.

                “Can I help you, stranger?” he asked. “You lost?”

                He already knew the answer would be _no_ and when the cloaked stranger shook their head in the negative, he felt his stomach start to drop. Then the stranger held up a pair of photographs in their right hand and immediately confirmed his worst fear.

                The stranger – a teenaged boy and hideously familiar-sounding – asked, “Have you seen these two?”

                Isoji didn’t need to look at the photos for more than half a second; he’d known what they were going to be the second that boy pulled them out. He knew the faces in those Bingo Book photos better than anyone save Juniko. He deliberately sniffed, looking away, and prayed she’d sensed the danger. “Not sure I can help you there, kid. We don’t see many folks out here. You might have better luck in town.”

                Out of the corner of his eye, he watched the stranger look at the photos in his hand, as if he didn’t quite understand the problem, and then the stranger shoved the photos back at him, his whole arm extended. The action pulled back the cloak, exposing the boy’s wrist.

                There, tattooed in stark black ink, were the numbers _B3-116_ and the sight of it hit him like a savage kick to the gut.

                _One hundred and sixteen_ , Sage’s balls! They’d always suspected there might be more, but _this_ many?

                “Maybe it would help if you took a closer look?” the stranger asked. There wasn’t even an ounce of feeling in the words.

                _This_ was what they were supposed to be, what they were made for.

                And he – he was going to die, right here, _today_.

                Isoji wanted to scream in rage. It wasn’t fair. He didn’t want to die. He didn’t want his wife to die. He and Juniko were good people and they’d done nothing wrong except exist. They’d stayed out of the way and they’d kept quiet, never getting involved even when the War was raging around their heads. They hadn’t been bothering anyone and _never_ once had they revealed the secret of their existence in all this time. Why come for them? Why now, after all these years? They were _happy._ And to send one of _them_ to do the job…?

                It wasn’t fair at all.

                Instead, he reached out to take the photos with his right hand, the faded proof of their common origin visible. It had been a long time since he had been _B2-012_ and, now, he was so much more than that: he was also Isoji Namaki. He looked at the photographs, at the two teens whose visage he and his wife had once mirrored so long ago and whose misfortune had led to he and his wife having these fifteen years of happiness, and he wondered. Then, he raised his eyes, the same dark grey as he knew the boy in front of him had, and sought them out, staring into the shadows cast by that hood.

                “Tell me,” Isoji said at last, his voice oddly calm even to himself. “What will you do when you run out of us to kill? Will they make you turn the blade on yourself?”

                The boy didn’t answer.

                Isoji watched as the boy drew his sword, the arc of the gleaming blade speeding towards him in seemingly slow motion, caught the flash of black-flecked red eyes reflected in the metal, and let his death come.

**Notes for the Chapter:**

> This expands off of the final chapter of Replica, though it is not necessary to read that to understand this story, as the situation will explain itself.
> 
> Isoji writes his name as 亥十二, while his wife, Juniko, writes hers as 十二子. Both contain 十二, or twelve, which reflects the serial number they're marked with. They write their chosen family name as 生木, which refers to green wood.


	2. Chapter 1

            He is standing in a field.

            There is a figure in a black, hooded cloak in front of him.

            _“Tell me,”_ a voice says, _“What will you do when you run out of us to kill?”_

            He looks down and there’s a blade stuck through his stomach, the hand of the cloaked figure holding the hilt. He raises his head, staring into piercing Sharingan red eyes in a pale face framed with messy black hair, and reaches for the face of the cloaked figure. His fingers brush cloth – a mask – and he pulls as his knees buckle beneath him.

            _“Will they make you turn your blade on yourself?”_ the voice asks.

            The face that stares down at him with cold and distant eyes is _his own._

 

* * *

 

            He sits up in his bunk with a start, his heartbeat pounding like thunder in his ears. His hand drifts to his stomach, but his fingers find only smooth skin, and, shakily, he runs a hand through his hair.

            The intercom crackles.

            “One-One-Six Alpha, your heart rate is elevated. What is your status?”

            In the bunk across from him, his partner stirs slightly and rolls onto her side to look at him with red eyes. His eyes flick from her to the camera mounted above the door, its lens trained on him. The red light below the lens is on.

            “Functional,” he replies.

            The camera lens shifts. It then returns to the center position and the red light blinks off.

            His fingers again drift towards his stomach.

            “What’s wrong?” his partner whispers.

            He hesitates and then leans back, staring up at the blank white ceiling. “Nothing,” he whispers back at last.

            _“Tell me. What will you do...?”_ the voice, older but still so very familiar, echoes in his ears, though its owner is dead.

            He closes his eyes, ignoring it, and tries to go back to sleep.

            He still feels the blade piercing him.

           

* * *

 

            One-One-Six Alpha wakes up automatically several hours later and blinks wearily, before standing and approaching his locker. He is unused to this sensation and, idly, he wonders if the previous night’s _aberration_ is responsible for his current state. He is still functional regardless and so deems it irrelevant.

            He and his partner dress in their black standard uniforms and assist each other in securing their armor and weapons. Her red hair is coming loose from her braid and he quickly addresses this, reweaving it into a tighter braid. The last items they don are their black half-masks and the black cloaks.

            “One-One-Six Alpha, ready,” he says.

            “One-One-Six Bravo, ready,” she says.

            The camera above the door focuses on them, the red light on.

            “One-One-Six, you are clear to proceed to Section 7,” the intercom announces.

            “Affirmative,” they both answer.

            The door slides open with a hydraulic hiss.

            They step out one at a time, him first, and then stand beside each other outside the door, facing the opposite side of the hall. Across from them, team One-One-Seven mirrors them perfectly. The door closes and they turn 90 degrees to their left, allowing them to see the backs of team One-One-Four. On the opposite side of the hall, the other teams turn 90 degrees to their right in perfect precision.

            As one, they move forward towards Section 7.

 

* * *

 

            Their handler is Mister Green. He is a skinny, sharp-faced man in a crisp white uniform and stares at them through thin-framed glasses. A plastic-coated badge displays his photo, a bar code, and a logo. On his desk are neat stacks of files.

            The door hisses closed and they stand at attention in front of the desk.

            “One-One-Six, at ease,” Mister Green says.

            Immediately, they widen their stances, dropping their arms behind their backs.

            “One-One-Six, you have a new mission,” Mister Green pauses, opening a folder in front of him. He skims it, spins it around and pushes it towards them, adding, “You will proceed to the following location and terminate the target. Report to Section 7 West Elevator.”

            One-One-Six Alpha picks up the folder and, in tandem, he and his partner reply, “Yes, sir.”

            “You are dismissed,” Mister Green says and presses a button.

            The door hisses open.

            One-One-Six exits in single file, passing by the waiting team One-One-Seven.

* * *

 

            The target is a male businessman of average build, aged forty-nine, and lives alone in a town about a half day’s journey from base. He resides in the penthouse of a moderately expensive apartment building and has hired several chuunin to protect him. With a quick scout of the perimeter, they are able to determine the hired ninja are from Konoha.

            One-One-Six Bravo guides Alpha past the chuunin by radio from the rooftop of a nearby building. Ten times she orders him to stop, relocate, and then gives the all-clear to move on and disarm the traps. When she informs him that the chakra of the last guard has moved past his position, he makes his move, slipping into the bedroom. It is there that he finds his target in bed, sleeping soundly.

            There is a moment when he presses his hand over the target’s mouth and nose where the target regains consciousness and stares at him in horrified recognition. The target begins to struggle, so he presses down harder and leans his full weight onto the target’s chest. He does not move until the target has ceased all movement.

            “Alpha, target chakra has ceased,” his earpiece buzzes.

            “Affirmative, Bravo,” he responds quietly into his throat mic.

            “Alpha, commence sanitation and proceed to Checkpoint Two,” comes her next response.

            “Affirmative, Bravo,” he says quietly and moves towards the center of the room.

            He sets up a small bundle and fixes several explosive notes on a short timer to it, activating them. He then moves towards the window, disables two more traps and slides the curtains open. They flutter ominously as moonlight cuts a swath of light across the room and, out of the corner of his eye, he notes a flash of light.

            He turns, shuriken in hand, and stops when he sees no threat.

            It’s only a badge on the desk, covered in plastic.

            One-One-Six Alpha silently approaches the desk and picks it up. The logo on it is identical to the one Mister Green wears, but the barcode and layout are different. The photo matches that of the target. He puts it back down, heads to the window, slides it open and leaves.

            The explosion shatters several windows on neighboring buildings, but they are already halfway across the city by that time.

 

            “Report,” Mister Green orders.

            “Target eliminated, sir,” One-One-Six Alpha responds. “Contact with non-target hostiles was avoided.”

            Mister Green nods, making a note in the folder. “Anything else to add?”

            “The non-target hostiles were from Konoha, sir,” Bravo notes, “Five, approximately chuunin rank.”

            Mister Green’s hand pauses. “Nothing unusual occurred, did it?”

            “No, sir,” Bravo states, “The mission was completed within optimal parameters.”

            “Very good,” Mister Green says and presses the button to open the door. “Excellent job, One-One-Six. You are dismissed. You may return to your bunk.”

            “Yes, sir,” they say in chorus and leave.

 

* * *

 

            The door to their room slides closed and they help each other out of their gear. One at a time, they clean themselves up in their small washroom and dress in their sleep uniforms. They then lie down in their bunks and, eventually, Bravo’s breathing evens out into a sleep rhythm.

            Alpha stares at the blank ceiling.

            The target’s horrified expression lingers in his mind with a perplexing intensity. He supposes it might be that the target had recognized him and had the same logo on his badge as their handler. But Alpha is unable to remember ever seeing the target before that file had been handed to them. Additionally, Alpha doesn’t understand why he should think of it. He has killed targets many times before and they have never crossed his mind again.

            _“What will you do when you run out of us to kill?”_

            For a moment, the memory of another recent target’s face flashes in his mind.

            Alpha rolls onto his side, blinking. He doesn’t understand why he is thinking of this now. It’s not like him.

            The number _B3-116_ is stark on his right wrist and he reaches up to rub it absently, recalling another set of numbers, _B2-012_ , in faded black ink on that target’s wrist.

            _“Will they make you turn your blade on yourself?”_

            The target was in his thirties, with longer, dark black hair and dark grey eyes, but Alpha knows the face very well. It was very much like the one he has seen in reflected in Bravo’s glasses before they put on the masks, only older.

            His stomach curdles and he briefly wonders if he is malfunctioning. Yes, he supposes, it has to be a malfunction. That would explain this _aberration_.

            And yet there is nothing wrong with him that he can specifically quantify.

            _“Tell me, what will you do...?”_

            Alpha closes his eyes.


	3. Chapter 2

            Alpha wakes with a start, instantly alert. It takes a few moments before he realizes he is in his bunk and then, blinking, he begins to relax.

            Bravo is already awake and sitting up, her red eyes fixed on him in silent contemplation.

            The camera above the door moves, red light on, and a voice calls over the intercom: “One-One-Six Alpha, your heart rate is elevated. What is your status?”

            “Functional,” he replies automatically and, again, the camera returns to its previous position before shutting off.

            Bravo continues to stare at him. At last, she says, “This is the second time that’s happened.”

            He says nothing.

            “Your chakra felt strange,” she adds, frowning. “I woke up and your eyes were moving, but they weren’t open. Your breathing was also shallow for a few moments before you woke.”

            “It’s an aberration,” he states. He doesn’t know quite how else to explain it because he doesn’t understand _why_ he can’t stop thinking about that target or how it is managing to affect him physically. There’s no logical reason for this to happen: he knows that he is completely functional and has sustained no physical damage. And yet, it has happened again and, this time, it’s much _worse_ than before.

            She cocks her head to the side, brows furrowed questioningly, but he still does not know how to explain it and says nothing.

            _“You and I are flesh and blood.”_

            He closes his eyes, willing away the shadowy image of his reflection standing in front of him.

            There is a heavy silence.

            “Bravo, have you ever thought about our targets? After the mission is finished?” he says at last, looking at her.

            She is quiet for a moment. “No.”

            “Oh,” Alpha says, frowning.

            There is another long silence.

            “Alpha,” Bravo pipes up.

            He looks at her, blinking.

            She gives him a serious look and says, “Don’t tell anyone about this _aberration._ ”

            He nods.

           

 

* * *

 

            It is still dark when they are woken for morning drills. Once again, they prepare by donning their uniforms, masks and armor. Alpha hesitates a little as Bravo reaches to secure the pieces of his armor that he cannot reach himself. It is strange and, stranger still, he feels an unfamiliar sensation when she chooses not to say anything. It lingers even well past their final armor check and stays with him all through the march to the training grounds, where they split off into their drill groups. It is yet another aberration and he understands it even less than he does the first, so he ignores it and focuses on the drills.

            Every draw of his sword is a killing blow that cleaves the air in a precise arc. His movements are efficient, tight, and fluid. It is as natural as breathing. Thoughts of the aberrations he is experiencing disappear with each familiar stroke of the blade and soon, nothing else exists beyond the space where he stands in the drill line: there is only him and the sword.

            When they are done, he rejoins Bravo for the march to morning mess. She briefly gives him a look and blinks twice, tilting her head before she closes her eyes and returns her head forward.

            _You are feeling better; that is good_ , he translates silently.

            Alpha mentally agrees.

 

* * *

 

            “One-One-Six, report to Mister Green after mess.”

            Alpha and Bravo look up from their food simultaneously. On their right, One-One-Four and One-One-Two freeze in place. All movement at the other nearby table stops as well.

            The speaker is an Alpha, kitted in the exact same armor and mask as them, and he has a Bravo at his side, just the same as the rest of them. They are both a little older than the units at this table, clearly from an earlier numerical group, and their Bravo is missing her right eye, if her eye patch and thick facial scarring are any indication. But it is this particular Alpha that commands everyone’s complete attention. There is something very different about him and everyone knows it, not just the Bravo sensors.

            Somehow, this Alpha just doesn’t feel _right._

            “Affirmative, One-Zero-Eight,” Bravo responds at last, reading their number from their chakra. “We will comply.”

            Alpha One-Zero-Eight looks at them for a moment, his head tilting to the side, and Alpha One-One-Six inexplicably feels his heart start to pound wildly in his chest, his appetite immediately vanishing as his stomach drops. It takes every ounce of control he has to quell the instinct to activate his eyes in response to the other’s gaze. Finally, the older Alpha nods and turns to leave, his Bravo trailing quietly after him.

            Not one unit moves until after One-Zero-Eight has left the mess hall.

            This time, Alpha knows he is not alone in not having a name for the sensation that older Alpha raises in him. He can see it in the shaken, ashen gazes of the other units. It is familiar and then, suddenly, he knows where he has seen it before: it is the same look he saw in the eyes of his last target.

            The realization instantly kills what little he’d regained of his appetite.

 

* * *

 

            Mister Green is waiting for them at his desk, a single open file folder resting in front of him. His expression is pinched and one of the muscles in his jaw twitches slightly when they enter.

            “One-One-Six, at ease,” he orders.

            They comply, immediately slipping into the widened stance and resting their arms behind their backs.

            “One-One-Six, you have a new mission,” Mister Green says, standing. “You will report to Mister Blue in Fair Water City for your mission objective.”

            He slides a small slip of paper across the desk.

            “Your confirmation codes,” he says. “Memorize them.”

            Alpha picks up the paper, pulling the minimum amount of chakra to his eyes for the Sharingan, and memorizes the words. He then deactivates it, returning to at ease.

            “Report to Section 7 East Gate,” Mister Green says, pressing a button. “Dismissed.”

            They exit, silently passing by One-One-Two.

            Never once do they make eye contact, but long after they are out of sight, Alpha can still feel their eyes on their backs.


	4. Chapter 3

                Fair Water City is two days chakra-enhanced run due east from the facility. It’s a smaller city than the last one they were in, but it is still the largest population center in the immediate area and serves as a major trade hub for the people from the many smaller towns and small farms scattered all throughout the hilly, heavily forested region to the north and east of the city. Additionally, it’s the last port on the Hagoromo River before the river narrows and turns south for the notorious Valley of the End and, supposedly, the great hidden village of Konoha.

                Alpha and Bravo move light and fast, avoiding the well-traveled roads and numerous shinobi pathways dotting the countryside.   When they camp, it is only for short intervals and with the utmost discretion. Their handlers have always made it clear that their priority is to make no contact with any party outside of their mission parameters and they stick to that training. Bravo ensures that they are long gone before any trouble has a chance to spot them, much less get close.

                Even so, Alpha doesn’t like this area. It’s too well-traveled by shinobi and the proximity to a hidden village puts them at a clear tactical disadvantage. More than that, there is something about the area itself that puts him on edge, a strange constant sense of familiarity where there should be none. He and Bravo have only ever passed through here once before, on their way northeast, and they certainly hadn’t stayed long enough that it should have made a lasting impression.

                _“What will you do when you run out of us to kill?”_

                Alpha grimaces and he notices Bravo briefly turn her head to regard him.

                The last leg of the journey can’t come quick enough for him.

 

* * *

 

                Mister Blue is round-faced with beady eyes and short, reddish-brown hair. His expression is sour and he hardly pays them much more than a glance before turning back to his binoculars and the small apartment window.

                “The situation has changed,” he says, waving a hand dismissively. “Operations are on hold until further notice.”

                Alpha and Bravo exchange a look. Alpha then asks, “Orders, sir?”

                Mister Blue lets out a long, nasal sigh, and peers over his shoulder at them. “Wait for the situation to change, _obviously_.”

                Then, under his breath as he turns away, Mister Blue adds: “Honestly, _this_ is why I hate these stupid things. Can’t even _think_ for themselves.”

                Bravo’s lips turn down at the corners and her brow furrows, but she does not say anything.

                “In the meantime,” Mister Blue pipes up again, “You can do whatever you’d like, as long as you keep a low profile and don’t _bother_ me. There’s money and clothes in the dresser if you need to go out for food or stretch your legs. Keys are on the table.”

                With that said, Mister Blue turns his back on them and leaves them to their own devices.

 

* * *

 

                It is a strange thing, Alpha thinks, to have to wait on a mission like this. He doesn’t much care for it. He finds that his thoughts keep drifting back to that target, more and more, and it doesn’t make any sense. Worse, he can’t seem to make the thoughts go away.

                Drills had helped before, he knows that, but that is not an option. There is nowhere in the building that is suited to practicing drills, save for the roof, and that is less than ideal, as it is in plain sight of several well-traveled ninja roof-paths. He considers finding something else to occupy himself, but there is little to do in the small apartment that does not manage to annoy Mister Blue and he has made it clear that he wants to have nothing to do with Alpha and Bravo until it is absolutely necessary to do so.

                Alpha pauses in his pacing, spotting the keys.

                “I’m going to stretch my legs,” he tells Bravo abruptly.

                “Don’t go too far,” she warns him. “Remember our orders.”

                He nods in the affirmative, pulling the hood of his cloak over his head.

                Keep a low profile: he can do that.

 

* * *

 

                Fair Water City could easily be described as a rabbit’s warren, in terms of layout. The old port city had been around in some form or another well before the Warring States and had been rebuilt numerous times over the years as wars ravaged the countryside. The result had produced a strange, incongruous mixture of traditional and modern architecture, all struggling to occupy the same space, and streets that had once led one way now ended abruptly or went nowhere at all. It was a highly advantageous situation for a ninja and no doubt why there were so many ninja pathways and hidden safe houses scattered throughout the city.

                A ninja could, if they wanted, hide in a different safe house every day for a year in Fair Water City and still not have been to them all.

                Mister Blue’s apartment is in the northeast of the city, right near the heart of the merchant quarter.   The building itself is rather nondescript, one of several identical looking apartment buildings tightly packed onto the block, and there’s hardly any room between it and the buildings next door. The next street over is lined with stores and market stalls, small hotels and hidden gambling dens. Up the street and around the corner, the two streets converge with several others, feeding into a large square, known as the North Market. Larger storefronts and shops surround the perimeter of the square, while smaller vendor stands form a tight ring within. A single police station squats on the far side, the plain and tall modern building seeming rather out of place amid older, squat glass storefronts. It is crowded and noisy. Every so often, there is the sound of a ship’s horn from the harbor.

                Alpha moves through the market crowds quietly, keeping on his guard. He keeps his hands in his pockets, in easy reach of the throwing knives he’d brought with him, and hunches his shoulders, keeping his face concealed by the shadow of his hood.

                The city is neutral territory for the most part and well-patrolled by the local police, who have special permission from the daimyo to openly carry katana, but the Konoha ninja still have a strong presence here.  His handlers had made it no secret that the police _would_ defer to the Konoha ninja if he or Bravo were to be discovered and that the consequences of being caught alive by them would be worse than death. Both he and Bravo had been issued poison capsules for that express scenario.

                But he isn’t thinking about that.

                Even though there are certainly plenty of distractions to occupy himself with in the market, his thoughts invariably find their way back to that target.

                So, he keeps walking, wandering further and further out into the city, trying to figure out why his thoughts keep turning in on themselves and getting absolutely nowhere, until he notices the buildings getting shorter and farther apart. He realizes that he is on the edge of the city, on the mouth of the road heading northeast.

                Alpha stares at the road. From here, he knows it’s a relatively short chakra-enhanced run to the place where that target used to live. He could be there and back easily.

                But why?

                He pauses, hesitating, and frowns. Why is he thinking of going back there? There is no reason to. After he’d killed the targets, he and Bravo had brought them back to the farmhouse and burned everything. There would be only ashes.

                Alpha shoves his hands in his pockets, letting out a harsh puff of air, and scowls, slowly pacing back and forth. It doesn’t make any sense, he thinks, and the fact that it doesn’t only makes him feel odd, as if he were malfunctioning in some capacity. He doesn’t like the feeling at all.

                At last, he stops, giving one last long look at the road, and starts the long walk back to the apartment.


End file.
